RetrogeneDB ID: retro_cjac_1327

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:23159992..23160321(+)
• Located in intron of: ENSCJAG00000002465

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000006661
• Aliases: None
• Description: None

Sequence

>retro_cjac_1327
GTGGCTCCTGTAGGGGTGCAAAGAAGCATGGCTGGGATCTAAGCTAGGGCTCTGTCTGGGCTGTGGCCCCAGCTGGATGC
TGTCATGAAACTCATTGCTGCCAAATACCTCCAGGGAAAGCTGCAGCAGGACCTGGAGGTGGAGGACGTGACCCTCAACC
ATTGTGGGTGCAGCTTCTGAGTCCTGGTGGTGTCGGCCAAGTTTGAGGGGAAGGTGCTGCTTCAGAGACAACGGCGGGTG
AATGTGTGCCTAGCCGGAAGCTCCCGCACATCCGTGCCTTTGAGCAGAAAACCCTGACCCCAGAGCAGTAGGCCTTTGAG
GGGCAGAAA

Alignment

ORF - retro_cjac_1327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.12 %
• Parental protein coverage: 76.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAPVRAQSPVAGVLAGVLSPLGYRPGWHTAMELSAEYLREKLQRDLEAEHVEVEDTTLNRCACSFRVLVV
          VAPV..Q...AG..A..LS..G..P.....M.L.A......LQ..L.....EVED.TLN.C.CSF.VLVV
Retrocopy VAPVGVQRSMAGI*ARALS--GLWPQLDAVMKLIAA---KYLQGKLQQD-LEVEDVTLNHCGCSF*VLVV

Parental  SAKFEGKPLLQRHRLVNACLA-EELPQIHAFEQKTLTPEQWARERQK
          SAKFEGK.LLQR.R.VN.CLA...LP.I.AFEQKTLTPEQ.A.E.QK
Retrocopy SAKFEGKVLLQRQRRVNVCLA<RKLPHIRAFEQKTLTPEQ*AFEGQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.11 RPM	3.55 RPM
SRP051959_heart	0.07 RPM	2.61 RPM
SRP051959_kidney	0.07 RPM	5.77 RPM
SRP051959_liver	0.04 RPM	3.18 RPM
SRP051959_lung	0.07 RPM	3.42 RPM
SRP051959_lymph_node	0.09 RPM	4.82 RPM
SRP051959_skeletal_muscle	0.02 RPM	3.10 RPM
SRP051959_spleen	0.15 RPM	4.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1327 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1327 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1522
Pongo abelii	retro_pabe_2326

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006661	1 retrocopy	retro_cjac_1327 ,
Echinops telfairi	ENSETEG00000006548	1 retrocopy	retro_etel_457,
Homo sapiens	ENSG00000169627	1 retrocopy	retro_hsap_2644,
Gorilla gorilla	ENSGGOG00000012724	2 retrocopies	retro_ggor_1847, retro_ggor_75,
Loxodonta africana	ENSLAFG00000017910	1 retrocopy	retro_lafr_712,
Myotis lucifugus	ENSMLUG00000003449	1 retrocopy	retro_mluc_2380,
Macaca mulatta	ENSMMUG00000007331	3 retrocopies	retro_mmul_1344, retro_mmul_1522, retro_mmul_1752,
Monodelphis domestica	ENSMODG00000015658	1 retrocopy	retro_mdom_1704,
Nomascus leucogenys	ENSNLEG00000001018	2 retrocopies	retro_nleu_1222, retro_nleu_650,
Oryctolagus cuniculus	ENSOCUG00000007562	1 retrocopy	retro_ocun_241,
Ochotona princeps	ENSOPRG00000002109	2 retrocopies	retro_opri_243, retro_opri_492,
Pongo abelii	ENSPPYG00000007237	2 retrocopies	retro_pabe_1608, retro_pabe_2326,
Pan troglodytes	ENSPTRG00000007990	2 retrocopies	retro_ptro_1284, retro_ptro_1781,
Rattus norvegicus	ENSRNOG00000047988	2 retrocopies	retro_rnor_322, retro_rnor_379,
Sorex araneus	ENSSARG00000003579	2 retrocopies	retro_sara_106, retro_sara_278,
Tarsius syrichta	ENSTSYG00000006274	1 retrocopy	retro_tsyr_1321,
Tursiops truncatus	ENSTTRG00000005543	2 retrocopies	retro_ttru_127, retro_ttru_1700,